Tests of gene order from three-locus linkage data

Exact tests for gene order are derived and compared for three loci using linkage data from phase-known, completely informative marker loci (i.e. parents are heterozygotes with at most one allele identical at each locus), or from triple back-cross matings. A simulation method, based on resampling genotypes of children, is introduced to obtain approximations to the distribution of the test statistics for general mating types in families consisting of children and parents, with or without grandparents, as are used in many studies in human gene mapping. The method is illustrated by an application to linkage data on chromosome 13.